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Toward understanding the conformational dynamics of RNA ligation.

Swift RV, Durrant J, Amaro RE, McCammon JA - Biochemistry (2009)

Bottom Line: This study describes a recent 70 ns molecular dynamics simulation of TbREL1, an ATP-dependent RNA-editing ligase of the nucleotidyltransferase superfamily that is required for the survival of T. brucei insect and bloodstream forms.In this work, a model of TbREL1 in complex with its full double-stranded RNA (dsRNA) substrate is created on the basis of the homologous relation between TbREL1 and T4 Rnl2.Important features of RNA binding and specificity are revealed for kinetoplastid ligases and the broader nucleotidyltransferase superfamily.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, NSF Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California 92093-0365, USA.

ABSTRACT
Members of the genus Trypanosoma, which include the pathogenic species Trypanosoma brucei and Trypanosoma cruzi, edit their post-transcriptional mitochondrial RNA via a multiprotein complex called the editosome. In T. brucei, the RNA is nicked prior to uridylate insertion and deletion. Following editing, nicked RNA is religated by one of two RNA-editing ligases (TbREL). This study describes a recent 70 ns molecular dynamics simulation of TbREL1, an ATP-dependent RNA-editing ligase of the nucleotidyltransferase superfamily that is required for the survival of T. brucei insect and bloodstream forms. In this work, a model of TbREL1 in complex with its full double-stranded RNA (dsRNA) substrate is created on the basis of the homologous relation between TbREL1 and T4 Rnl2. The simulation captures TbREL1 dynamics in the state immediately preceding RNA ligation, providing insights into the functional dynamics and catalytic mechanism of the kinetoplastid ligation reaction. Important features of RNA binding and specificity are revealed for kinetoplastid ligases and the broader nucleotidyltransferase superfamily.

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Nicked dsRNA bound to TbREL1, poised to catalyze religation. A unique kinetoplastid insert is colored yellow, and a cluster of residues thought to be important in RNA recognition on the 5′-PO4 side of the nick is colored orange. The magnified inset shows protein residues that make stabilizing contacts with the RNA.
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fig1: Nicked dsRNA bound to TbREL1, poised to catalyze religation. A unique kinetoplastid insert is colored yellow, and a cluster of residues thought to be important in RNA recognition on the 5′-PO4 side of the nick is colored orange. The magnified inset shows protein residues that make stabilizing contacts with the RNA.

Mentions: Motivated by the close homology between Rnl2 and TbREL1 and the desire to understand the functional dynamics of the kinetoplastid ligation reaction, we investigate the conformational dynamics of TbREL1 in complex with a nicked dsRNA substrate in its canonical A-form. On the basis of the homologous structural and functional relationships between TbREL1 and T4 Rnl2, we develop a model of a nicked dsRNA−TbREL1 complex (Figure 1) and perform an all-atom explicitly solvated molecular dynamics simulation of the system. The integration of RNA into MD simulations has benefited from recent improvements in both force field development and algorithms (16,17), allowing us to gain insights into the dynamics and catalytic mechanism. The simulated system contains AMP attached to the nick 5′-PO4 moiety (AppN), characteristic of the step 2 intermediate (13). The non-nicked strand represents the template, or gRNA, and the nicked strand represents the post-transcriptionally modified pre-mRNA. Fluctuations of conserved interactions between the enzyme and RNA substrate, as well as the dynamics of conserved active site residues, are examined and discussed in the context of step 3 of the religation mechanism. Furthermore, we explore the effect of a unique kinetoplastid insert region on dsRNA binding.


Toward understanding the conformational dynamics of RNA ligation.

Swift RV, Durrant J, Amaro RE, McCammon JA - Biochemistry (2009)

Nicked dsRNA bound to TbREL1, poised to catalyze religation. A unique kinetoplastid insert is colored yellow, and a cluster of residues thought to be important in RNA recognition on the 5′-PO4 side of the nick is colored orange. The magnified inset shows protein residues that make stabilizing contacts with the RNA.
© Copyright Policy - open-access - ccc-price
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651658&req=5

fig1: Nicked dsRNA bound to TbREL1, poised to catalyze religation. A unique kinetoplastid insert is colored yellow, and a cluster of residues thought to be important in RNA recognition on the 5′-PO4 side of the nick is colored orange. The magnified inset shows protein residues that make stabilizing contacts with the RNA.
Mentions: Motivated by the close homology between Rnl2 and TbREL1 and the desire to understand the functional dynamics of the kinetoplastid ligation reaction, we investigate the conformational dynamics of TbREL1 in complex with a nicked dsRNA substrate in its canonical A-form. On the basis of the homologous structural and functional relationships between TbREL1 and T4 Rnl2, we develop a model of a nicked dsRNA−TbREL1 complex (Figure 1) and perform an all-atom explicitly solvated molecular dynamics simulation of the system. The integration of RNA into MD simulations has benefited from recent improvements in both force field development and algorithms (16,17), allowing us to gain insights into the dynamics and catalytic mechanism. The simulated system contains AMP attached to the nick 5′-PO4 moiety (AppN), characteristic of the step 2 intermediate (13). The non-nicked strand represents the template, or gRNA, and the nicked strand represents the post-transcriptionally modified pre-mRNA. Fluctuations of conserved interactions between the enzyme and RNA substrate, as well as the dynamics of conserved active site residues, are examined and discussed in the context of step 3 of the religation mechanism. Furthermore, we explore the effect of a unique kinetoplastid insert region on dsRNA binding.

Bottom Line: This study describes a recent 70 ns molecular dynamics simulation of TbREL1, an ATP-dependent RNA-editing ligase of the nucleotidyltransferase superfamily that is required for the survival of T. brucei insect and bloodstream forms.In this work, a model of TbREL1 in complex with its full double-stranded RNA (dsRNA) substrate is created on the basis of the homologous relation between TbREL1 and T4 Rnl2.Important features of RNA binding and specificity are revealed for kinetoplastid ligases and the broader nucleotidyltransferase superfamily.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, NSF Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California 92093-0365, USA.

ABSTRACT
Members of the genus Trypanosoma, which include the pathogenic species Trypanosoma brucei and Trypanosoma cruzi, edit their post-transcriptional mitochondrial RNA via a multiprotein complex called the editosome. In T. brucei, the RNA is nicked prior to uridylate insertion and deletion. Following editing, nicked RNA is religated by one of two RNA-editing ligases (TbREL). This study describes a recent 70 ns molecular dynamics simulation of TbREL1, an ATP-dependent RNA-editing ligase of the nucleotidyltransferase superfamily that is required for the survival of T. brucei insect and bloodstream forms. In this work, a model of TbREL1 in complex with its full double-stranded RNA (dsRNA) substrate is created on the basis of the homologous relation between TbREL1 and T4 Rnl2. The simulation captures TbREL1 dynamics in the state immediately preceding RNA ligation, providing insights into the functional dynamics and catalytic mechanism of the kinetoplastid ligation reaction. Important features of RNA binding and specificity are revealed for kinetoplastid ligases and the broader nucleotidyltransferase superfamily.

Show MeSH